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Yes manifolds are stock and are made of a cast, which is very rough in the inside creating a barrier for premium air flow. Manifolds are cheap and easier to make, that's why they use them. Headers are made of tubing which is a smooth surface to create a better path for air flow.
Also, the term manifold can be used for either intake or exhaust. Being a former Honda guy, whenever I hear manifold, I automatically think intake manifold. I haven't heard it used for exhaust until I got my stang.